size <- 12. Later this will be the number of rows of the matrix.x <- rnorm( size ).x1 by adding (on average 10 times smaller) noise to x: x1 <- x + rnorm( size )/10.x and x1 should be close to 1.0: check this with function cor.x2 and x3 by adding (other) noise to x.size <- 12
x <- rnorm( size )
x1 <- x + rnorm( size )/10
cor( x, x1 )
[1] 0.9980072
x2 <- x + rnorm( size )/10
x3 <- x + rnorm( size )/10
x1, x2 and x3 column-wise into a matrix using m <- cbind( x1, x2, x3 ).m.m.heatmap( m, Colv = NA, Rowv = NA, scale = "none" ).m <- cbind( x1, x2, x3 )
class( m )
[1] "matrix"
head( m )
x1 x2 x3
[1,] -0.7950809 -0.8939090 -1.0125544
[2,] 0.4604709 0.5728760 0.4927988
[3,] -1.4088353 -1.6094224 -1.5706379
[4,] -0.4584021 -0.2685923 -0.2029335
[5,] -2.0732808 -1.8952934 -2.1208334
[6,] 0.8189590 0.6867817 0.7351612
heatmap( m, Colv = NA, Rowv = NA, scale = "none" ) # high is dark red, low is yellow
# x1, x2, x3 follow similar color pattern, they should be correlated
y1…y4 (but not correlated with x), of the same length size.m from columns x1…x3,y1…y4 in some random order.y <- rnorm( size )
y1 <- y + rnorm( size )/10
y2 <- y + rnorm( size )/10
y3 <- y + rnorm( size )/10
y4 <- y + rnorm( size )/10
m <- cbind( y4, y3, x2, y1, x1, x3, y2 )
heatmap( m, Colv = NA, Rowv = NA, scale = "none" ) # high is dark red, low is yellow
cc <- cor( m ) to build the matrix of correlation coefficients between columns of m.round( cc, 3 ) to show this matrix with 3 digits precision.cc <- cor( m )
round( cc, 3 ) #
y4 y3 x2 y1 x1 x3 y2
y4 1.000 0.992 -0.059 0.993 -0.068 -0.090 0.993
y3 0.992 1.000 -0.063 0.996 -0.075 -0.096 0.988
x2 -0.059 -0.063 1.000 -0.053 0.992 0.993 -0.071
y1 0.993 0.996 -0.053 1.000 -0.068 -0.088 0.990
x1 -0.068 -0.075 0.992 -0.068 1.000 0.994 -0.081
x3 -0.090 -0.096 0.993 -0.088 0.994 1.000 -0.109
y2 0.993 0.988 -0.071 0.990 -0.081 -0.109 1.000
heatmap( cc, symm = TRUE, scale = "none" )
# E.g. value for (row: x1, col: y1) is the corerlation of vectors x1, y1.
# Values of 1.0 are on the diagonal: e.g. x1 is perfectly correlated with x1.
# Correlations between x, x vectors are close to 1.0.
# Correlations between y, y vectors are close to 1.0.
# Correlations between x, y vectors are close to 0.0.
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